I decided to start providing regular updates on my Marie Curie research on this blog.
These are my plans for the next 6 months, the content is basically coming from email exchanges with my collaborators.
- Pedigree reconstruction in the marble trout population of Lipovesck. We have recently genotyped the individuals that have been sampled in 2013 (June and September) and 2014 (June and September). All samples have been sexed and I am ready to carry out the pedigree reconstruction, with particular focus on the post-2009 generation. In 2009, a huge flood hit Lipovesck and just a handful of marble trout survived. The main goal is to understand the recovery process after the flood, who reproduced and whether certain traits were related with higher chances of post-flood reproduction. Then, I'd like to test whether my predictions on post-flood recovery (younger age at reproduction due to the relaxation of density-dependent processes after an episode of massive mortality) were right. If it is true, we should expect the 2011 cohort to have reproduced (at least some individuals) in 2013, thus anticipating one year reproduction (at age 3 or 4 under normal conditions).
- Phylogeny of marble trout living in Western Slovenia. We are sequencing right now additional fish from the populations of Idirijca, Svenica, and Studenc. For Idirijca, the sequencing of additional individuals was motivated by the lack of a sufficient number of SNPs for pedigree reconstruction (96 SNPs recommended, ~80 should be enough). Fish from Svenica and Studenc have never been sequenced. In order to save some money, we tried to sequence fish from some of the populations part of the cluster identified by Fumagalli et al. 2002 (14 microsatellite loci were used). However, since almost none of the SNPs found in the populations of Trebuscica and Idrijca were found to be variable also in Svenica and Studenc, we now have the suspicion that Svenica and Studenc are not as genetically close to Trebuscica and Idrijca as reported by Fumgalli et al. After this sequencing run, we should have all the elements for studying the phylogeny of marble trout, inbreeding, loci under selection etc.
- Writing a technical paper on SNP discovery for marble trout. While we are still discovering and characterizing SNPs for the populations of Idirjca, Svenica and Studens, I am confident we will discover the population-specific panel of SNPs soon. The only real problem is the population of Huda, for which we found very little to almost non-existent polymorphism. Given money, we might try to sequence some fish from Huda using an Hi-seq machine (we are currently using a Mi-seq with size selection at 500 base pairs).
- Differences in life-histories (growth, survival, morphology) in marble trout, including density-dependent patterns, with the main focus on the relationship between growth and survival as possibly mediated by cannibalism. Most of the analysis have been done.